Working Results2
Kaushik Narasimhan
Sys.Date()
Summary Statistics
Species Information
## Species Mammal.Bird Func.group
## 1 agouti Mammal TD
## 2 brown four-eyed oppossum Mammal TD
## 3 Baudo guan Bird FD
## 4 crab eating racoon Mammal TD
## 5 choco toucan Bird FD
## 6 chestnut-mandibled toucan Bird FD
## 7 coati Mammal TD
## 8 collared peccary Mammal TD
## 9 Greater Tinamou Bird TD
## 10 kinkajou Mammal TD
## 11 oilbird Bird FD
## 12 opossum Mammal TD
## 13 paca Mammal TD
## 14 red brocket deer Mammal TD
## 15 Rose faced parrot Bird FD
## 16 rufous fronted wood-quail (Odontophorus erythrops) Bird TD
## 17 rodent spp. Mammal TD
## 18 rufous tree rat Mammal TD
## 19 Southern mealy parrot Bird FD
## 20 squirrel spp. Mammal TD
## 21 toucan spp. Bird FD
## 22 Tomes spiny rat Mammal TD
## 23 Umbrellabird Bird FD
## 24 Wood-rail Bird TD
## sightings ingestions removals nibbles detections
## 1 260 0 44 70 15
## 2 82 2 2 4 12
## 3 20 2 4 2 5
## 4 1 0 0 0 1
## 5 272 99 142 3 14
## 6 316 157 168 1 16
## 7 458 2 0 175 11
## 8 136 4 0 0 7
## 9 8 0 0 0 2
## 10 84 0 3 14 9
## 11 73 0 36 0 7
## 12 100 1 0 27 8
## 13 416 0 31 73 10
## 14 5 0 0 0 1
## 15 2 0 0 0 2
## 16 434 0 0 4 15
## 17 1380 0 197 45 21
## 18 5 0 0 1 1
## 19 10 0 7 0 1
## 20 675 0 249 109 20
## 21 284 75 85 0 15
## 22 136 0 24 1 6
## 23 269 34 96 2 20
## 24 127 0 0 7 10
Visualization of ht vs focal 50
Scatter plots using 50m
Scatter of Disperser visitation at 50m fruiting neighborhood
Correlation at each band
effect of height focal against visitation
## $vis.rate
##
## $FD.rate
##
## $TD.rate
PCA of all environmental variables
PCA of selected environmental variables
Constrained ordination
Models 50 m band
## [1] FIELD_TAG EAST NORTH ELEV num.close
## <0 rows> (or 0-length row.names)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: real.visitation ~ focalmonth..50 * Height + offset(lograte) +
## (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 3794.0 3815.6 -1890.0 3780.0 154
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -8.5540 -2.5265 -0.5044 1.5826 30.3127
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 2.055 1.433
## focalmonth..50 1.286 1.134 -0.59
## Number of obs: 161, groups: Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.33895 0.22232 -1.525 0.1274
## focalmonth..50 0.51673 0.28594 1.807 0.0707 .
## Heightlow 0.85863 0.04317 19.889 < 2e-16 ***
## focalmonth..50:Heightlow -0.27907 0.03740 -7.462 8.5e-14 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.435
## Heightlow -0.154 0.070
## fclmn..50:H 0.094 -0.101 -0.625## chisq ratio rdf p
## 3111.07024 20.20175 154.00000 0.00000## # Check for zero-inflation
##
## Observed zeros: 21
## Predicted zeros: 2
## Ratio: 0.10## # Overdispersion test
##
## dispersion ratio = 20.202
## Pearson's Chi-Squared = 3111.070
## p-value = < 0.001## Family: poisson ( log )
## Formula:
## real.visitation ~ focalmonth..50 * Height + offset(lograte) +
## (1 + focalmonth..50 | Tree)
## Zero inflation: ~focalmonth..50
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 3292.9 3320.6 -1637.4 3274.9 152
##
## Random effects:
##
## Conditional model:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 1.386 1.177
## focalmonth..50 1.358 1.165 -0.71
## Number of obs: 161, groups: Tree, 49
##
## Conditional model:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.04053 0.18870 0.215 0.8299
## focalmonth..50 0.51522 0.29570 1.742 0.0814 .
## Heightlow 0.72386 0.04371 16.561 < 2e-16 ***
## focalmonth..50:Heightlow -0.27525 0.03749 -7.341 2.12e-13 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Zero-inflation model:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.93240 0.27910 -6.924 4.4e-12 ***
## focalmonth..50 0.05273 0.22931 0.230 0.818
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## # Check for Multicollinearity
##
## Low Correlation
##
## Parameter VIF Increased SE
## focalmonth..50 1.01 1.01
## Height 1.59 1.26
## focalmonth..50:Height 1.60 1.26## Not enough model terms in the zero_inflated part of the model to check for multicollinearity.## # Check for Multicollinearity
##
## * conditional component:
##
## Low Correlation
##
## Parameter VIF Increased SE
## focalmonth..50 1.01 1.01
## Height 1.59 1.26
## focalmonth..50:Height 1.60 1.26## Not enough model terms in the zero_inflated part of the model to check for multicollinearity.
## Family: poisson ( log )
## Formula: real.visitation ~ focalmonth..50 * Height + focalmonth..50 *
## num.close + offset(lograte) + (1 + focalmonth..50 | Tree)
## Zero inflation: ~focalmonth..50
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 3293.4 3327.3 -1635.7 3271.4 150
##
## Random effects:
##
## Conditional model:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 1.381 1.175
## focalmonth..50 1.132 1.064 -0.74
## Number of obs: 161, groups: Tree, 49
##
## Conditional model:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.11705 0.28201 0.415 0.6781
## focalmonth..50 1.31714 0.52908 2.490 0.0128 *
## Heightlow 0.72446 0.04371 16.575 < 2e-16 ***
## num.close -0.01449 0.04175 -0.347 0.7285
## focalmonth..50:Heightlow -0.27479 0.03749 -7.330 2.3e-13 ***
## focalmonth..50:num.close -0.09392 0.06148 -1.528 0.1266
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Zero-inflation model:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.93225 0.27907 -6.924 4.39e-12 ***
## focalmonth..50 0.05267 0.22930 0.230 0.818
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Conditional model:
## Groups Name Std.Dev. Corr
## Tree (Intercept) 1.1753
## focalmonth..50 1.0641 -0.744## Not enough model terms in the zero_inflated part of the model to check for multicollinearity.## # Check for Multicollinearity
##
## * conditional component:
##
## Low Correlation
##
## Parameter VIF Increased SE
## focalmonth..50 3.91 1.98
## Height 1.59 1.26
## num.close 1.41 1.19
## focalmonth..50:Height 1.60 1.27
## focalmonth..50:num.close 4.67 2.16
## Not enough model terms in the zero_inflated part of the model to check for multicollinearity.
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.339 0.999 -0.34 0.734
## focalmonth..50 0.517 1.285 0.40 0.688
## Heightlow 0.859 0.194 4.43 9.6e-06 ***
## focalmonth..50:Heightlow -0.279 0.168 -1.66 0.097 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1